pdb¶

Bindings for core::io::pdb namespace

class pyrosetta.rosetta.core.io.pdb.Field¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.io.pdb.Field, : pyrosetta.rosetta.core.io.pdb.Field) → pyrosetta.rosetta.core.io.pdb.Field¶: C++: core::io::pdb::Field::operator=(const struct core::io::pdb::Field &) –> struct core::io::pdb::Field &

property end¶

set_value_from_pdb_line(self: pyrosetta.rosetta.core.io.pdb.Field, source: str) → None¶

Read field value from given .pdb line and set.

C++: core::io::pdb::Field::set_value_from_pdb_line(std::string) –> void

property start¶

property value¶

class pyrosetta.rosetta.core.io.pdb.RecordCollection¶

Bases: SingletonBase_core_io_pdb_RecordCollection_t

This class is a singleton and manages the definitions of PDB Records, which should only be read from the database one time.

static get_instance() → core::io::pdb::RecordCollection¶: C++: utility::SingletonBase<core::io::pdb::RecordCollection>::get_instance() –> class core::io::pdb::RecordCollection *

static is_valid_record_type(type: str) → bool¶

Is the given string a valid 6-letter PDB record type?

C++: core::io::pdb::RecordCollection::is_valid_record_type(const std::string &) –> bool

class pyrosetta.rosetta.core.io.pdb.RecordType¶

Bases: pybind11_object

Enumerators for all of the record types used in PDB files, according to:: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

Members:

HEADER

OBSLTE

TITLE

SPLIT

CAVEAT

COMPND

SOURCE

KEYWDS

EXPDTA

NUMMD

MDLTYP

AUTHOR

REVDAT

SPRSDE

JRNL

REMARK

DBREF

DBREF1

DBREF2

SEQADV

SEQRES

MODRES

HET

HETNAM

HETSYN

FORMUL

HELIX

SHEET

SSBOND

LINK

CISPEP

SITE

CRYST1

ORIGX1

ORIGX2

ORIGX3

SCALE1

SCALE2

SCALE3

MTRIX1

MTRIX2

MTRIX3

MODEL

ATOM

ANISOU

TER

HETATM

ENDMDL

CONECT

MASTER

END

UNKNOW

N_RECORD_TYPES

ANISOU = <RecordType.ANISOU: 45>¶

ATOM = <RecordType.ATOM: 44>¶

AUTHOR = <RecordType.AUTHOR: 12>¶

CAVEAT = <RecordType.CAVEAT: 5>¶

CISPEP = <RecordType.CISPEP: 31>¶

COMPND = <RecordType.COMPND: 6>¶

CONECT = <RecordType.CONECT: 49>¶

CRYST1 = <RecordType.CRYST1: 33>¶

DBREF = <RecordType.DBREF: 17>¶

DBREF1 = <RecordType.DBREF1: 18>¶

DBREF2 = <RecordType.DBREF2: 19>¶

END = <RecordType.END: 51>¶

ENDMDL = <RecordType.ENDMDL: 48>¶

EXPDTA = <RecordType.EXPDTA: 9>¶

FORMUL = <RecordType.FORMUL: 26>¶

HEADER = <RecordType.HEADER: 1>¶

HELIX = <RecordType.HELIX: 27>¶

HET = <RecordType.HET: 23>¶

HETATM = <RecordType.HETATM: 47>¶

HETNAM = <RecordType.HETNAM: 24>¶

HETSYN = <RecordType.HETSYN: 25>¶

JRNL = <RecordType.JRNL: 15>¶

KEYWDS = <RecordType.KEYWDS: 8>¶

LINK = <RecordType.LINK: 30>¶

MASTER = <RecordType.MASTER: 50>¶

MDLTYP = <RecordType.MDLTYP: 11>¶

MODEL = <RecordType.MODEL: 43>¶

MODRES = <RecordType.MODRES: 22>¶

MTRIX1 = <RecordType.MTRIX1: 40>¶

MTRIX2 = <RecordType.MTRIX2: 41>¶

MTRIX3 = <RecordType.MTRIX3: 42>¶

NUMMD = <RecordType.NUMMD: 10>¶

N_RECORD_TYPES = <RecordType.UNKNOW: 52>¶

OBSLTE = <RecordType.OBSLTE: 2>¶

ORIGX1 = <RecordType.ORIGX1: 34>¶

ORIGX2 = <RecordType.ORIGX2: 35>¶

ORIGX3 = <RecordType.ORIGX3: 36>¶

REMARK = <RecordType.REMARK: 16>¶

REVDAT = <RecordType.REVDAT: 13>¶

SCALE1 = <RecordType.SCALE1: 37>¶

SCALE2 = <RecordType.SCALE2: 38>¶

SCALE3 = <RecordType.SCALE3: 39>¶

SEQADV = <RecordType.SEQADV: 20>¶

SEQRES = <RecordType.SEQRES: 21>¶

SHEET = <RecordType.SHEET: 28>¶

SITE = <RecordType.SITE: 32>¶

SOURCE = <RecordType.SOURCE: 7>¶

SPLIT = <RecordType.SPLIT: 4>¶

SPRSDE = <RecordType.SPRSDE: 14>¶

SSBOND = <RecordType.SSBOND: 29>¶

TER = <RecordType.TER: 46>¶

TITLE = <RecordType.TITLE: 3>¶

UNKNOW = <RecordType.UNKNOW: 52>¶

property name¶

property value¶

pyrosetta.rosetta.core.io.pdb.add_to_multimodel_pdb(*args, **kwargs)¶

Overloaded function.

add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, model_tag: str) -> bool
add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, model_tag: str, clear_existing_structures: bool) -> bool

Adds a pose to a multimodel pdb file (or creates the file): Use default StructFileRepOptions

C++: core::io::pdb::add_to_multimodel_pdb(const class core::pose::Pose &, const std::string &, const std::string &, bool) –> bool

add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, model_tag: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> bool
add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, model_tag: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions, clear_existing_structures: bool) -> bool

Adds a pose to a multimodel pdb file (or creates the file)

C++: core::io::pdb::add_to_multimodel_pdb(const class core::pose::Pose &, const std::string &, const std::string &, class std::shared_ptr<const class core::io::StructFileRepOptions>, bool) –> bool

add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, model_tag: str) -> None

Adds a pose to a multimodel pdb file: Use default StructFileRepOptions

C++: core::io::pdb::add_to_multimodel_pdb(const class core::pose::Pose &, std::ostream &, const std::string &) –> void

add_to_multimodel_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, model_tag: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Adds a pose to a multimodel pdb file

C++: core::io::pdb::add_to_multimodel_pdb(const class core::pose::Pose &, std::ostream &, const std::string &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

pyrosetta.rosetta.core.io.pdb.build_pose_from_pdb_as_is(*args, **kwargs)¶

Overloaded function.

build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, filename: str) -> None

Builds a pose into <pose>, without repacking or optimizing: hydrogens; using the full-atom ResidueTypeSet

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const std::string &) –> void

build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, pdr_options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> None

Builds a pose into <pose>, without repacking or optimizing: hydrogens; using the full-atom ResidueTypeSet and a set of options.

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const std::string &, const class core::io::StructFileReaderOptions &) –> void

build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> None

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const std::string &) –> void

build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, pdr_options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> None

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const std::string &, const class core::io::StructFileReaderOptions &) –> void

build_pose_from_pdb_as_is(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, file_contents: pyrosetta.rosetta.std.istream, pdr_options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> None

C++: core::io::pdb::build_pose_from_pdb_as_is(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const std::string &, std::istream &, const class core::io::StructFileReaderOptions &) –> void

pyrosetta.rosetta.core.io.pdb.create_pdb_contents_from_sfr(*args, **kwargs)¶

Overloaded function.

create_pdb_contents_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep) -> str
create_pdb_contents_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> str

Create a full .pdb as a string given a StructFileRep object.

C++: core::io::pdb::create_pdb_contents_from_sfr(const class core::io::StructFileRep &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> std::string

pyrosetta.rosetta.core.io.pdb.create_records_from_pdb_file_contents(pdb_contents: str) → pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t¶

Create a list of .pdb format records from the entire contents of a .pdb file.

C++: core::io::pdb::create_records_from_pdb_file_contents(const std::string &) –> class utility::vector1<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > >, class std::allocator<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > > > >

pyrosetta.rosetta.core.io.pdb.create_records_from_pdb_lines(lines: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t¶

Create a list of .pdb format records from the lines from a .pdb file.

C++: core::io::pdb::create_records_from_pdb_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class utility::vector1<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > >, class std::allocator<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > > > >

pyrosetta.rosetta.core.io.pdb.create_records_from_sfr(*args, **kwargs)¶

Overloaded function.

create_records_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep) -> pyrosetta.rosetta.std.vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t
create_records_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> pyrosetta.rosetta.std.vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t

Create vector of records from given StructFileRep object.

C++: core::io::pdb::create_records_from_sfr(const class core::io::StructFileRep &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> class std::vector<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > >, class std::allocator<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > > > >

pyrosetta.rosetta.core.io.pdb.create_sfr_from_pdb_file_contents(*args, **kwargs)¶

Overloaded function.

create_sfr_from_pdb_file_contents(pdb_contents: str, options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> pyrosetta.rosetta.core.io.StructFileRep

Create a representation of structural file data from .pdb file contents with options.

C++: core::io::pdb::create_sfr_from_pdb_file_contents(const std::string &, const class core::io::StructFileReaderOptions &) –> class core::io::StructFileRep

create_sfr_from_pdb_file_contents(pdb_contents: str) -> pyrosetta.rosetta.core.io.StructFileRep

Create a representation of structural file data from .pdb file contents.

C++: core::io::pdb::create_sfr_from_pdb_file_contents(const std::string &) –> class core::io::StructFileRep

pyrosetta.rosetta.core.io.pdb.create_sfr_from_pdb_records(*args, **kwargs)¶

Overloaded function.

create_sfr_from_pdb_records(records: pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t, options: pyrosetta.rosetta.core.io.StructFileReaderOptions) -> pyrosetta.rosetta.core.io.StructFileRep

Create a representation of structural file data from a list of .pdb format records with options.

C++: core::io::pdb::create_sfr_from_pdb_records(class utility::vector1<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > >, class std::allocator<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > > > > &, const class core::io::StructFileReaderOptions &) –> class core::io::StructFileRep

create_sfr_from_pdb_records(records: pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t) -> pyrosetta.rosetta.core.io.StructFileRep

Create a representation of structural file data from a list of .pdb format records.

C++: core::io::pdb::create_sfr_from_pdb_records(class utility::vector1<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > >, class std::allocator<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > > > > &) –> class core::io::StructFileRep

pyrosetta.rosetta.core.io.pdb.dump_multimodel_pdb(*args, **kwargs)¶

Overloaded function.

dump_multimodel_pdb(poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, file_name: str) -> bool

Writes poses to a single PDB file, returns false if an error occurs: Use default StructFileRepOptions

C++: core::io::pdb::dump_multimodel_pdb(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, const std::string &) –> bool

dump_multimodel_pdb(poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, file_name: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> bool

Writes poses to a single PDB file, returns false if an error occurs

C++: core::io::pdb::dump_multimodel_pdb(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, const std::string &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> bool

dump_multimodel_pdb(poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, out: pyrosetta.rosetta.std.ostream) -> None

Writes poses to a given stream in PDB file format: Use default StructFileRepOptions

C++: core::io::pdb::dump_multimodel_pdb(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, std::ostream &) –> void

dump_multimodel_pdb(poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Writes poses to a given stream in PDB file format

C++: core::io::pdb::dump_multimodel_pdb(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, std::ostream &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

pyrosetta.rosetta.core.io.pdb.dump_pdb(*args, **kwargs)¶

Overloaded function.

dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str) -> bool

Writes <pose> to a PDB file, returns false if an error occurs: Use default StructFileRepOptions

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const std::string &) –> bool

dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> bool

Writes <pose> to a PDB file, returns false if an error occurs

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const std::string &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> bool

dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) -> None
dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, out_fname: str) -> None

Writes <pose> to a given stream in PDB file format: Use default StructFileRepOptions

If a non-empty string is given for the out_fname variable, then the Pose energy table at the bottom of the PDB will be labeled with this string.

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, std::ostream &, const std::string &) –> void

dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None
dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions, out_fname: str) -> None

Writes <pose> to a given stream in PDB file format: If a non-empty string is given for the out_fname variable, then the Pose energy table at the bottom of the PDB will be labeled with this string.

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, std::ostream &, class std::shared_ptr<const class core::io::StructFileRepOptions>, const std::string &) –> void

dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, mask: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> None
dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, mask: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

This version takes an AtomID mask.

Used by Will’s motif hash stuff, I think.

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, std::ostream &, const class core::id::AtomID_Map<bool> &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, std::ostream &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: pyrosetta.rosetta.utility.io.ozstream) -> None
dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: pyrosetta.rosetta.utility.io.ozstream, filename: str) -> None

Writes a pose to a given stream in PDB file format, optionally

appending a given string and optionally extracting scores from the pose.

This came out of the 2016 Chemical XRW. It’s an attempt to preserve some stuff that jd2 was doing before, while centralizing all PDB generation in one place.

The pose to turn into a PDB.

Additional data to append to the PDB file data (from the job).

The output stream that the PDB file data will be written to.

(Optional) String for the filename. Will be included in the score data table if provided.

NOTE: The two booleans are now specified in the StructFileRepOptions. Job data is no longer used in JD3. Do not use this function for general pdb writing. Use dump_file.

Vikram K. Mulligan (vmullig.edu).

Jared Adolf-Bryfogle (jadolfbr.com)

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const std::string &, class utility::io::ozstream &, const std::string &) –> void

dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: str) -> None
dump_pdb(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: str, filename: str) -> None

Writes a pose to a given string in PDB file format, optionally

appending a given string and optionally extracting scores from the pose.

This came out of the 2016 Chemical XRW. It’s an attempt to preserve some stuff that jd2 was doing before, while centralizing all PDB generation in one place.

The pose to turn into a PDB.

Additional data to append to the PDB file data from the Job.

The output string that the PDB file data will be written to.

(Optional) String for the filename. Will be included in the score data table if provided.

NOTE: The two booleans are now specified in the StructFileRepOptions. Job data is no longer used in JD3. Do not use this function for general pdb writing. Use dump_file.

Vikram K. Mulligan (vmullig.edu).

C++: core::io::pdb::dump_pdb(const class core::pose::Pose &, const std::string &, std::string &, const std::string &) –> void

pyrosetta.rosetta.core.io.pdb.dump_pdb_residue(*args, **kwargs)¶

Overloaded function.

dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue) -> str
dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> str
dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, options: pyrosetta.rosetta.core.io.StructFileRepOptions, start_atom_number: int) -> str

PyRosetta-Compatible; Writes pdb data for the given residue, beginning from the given atom number

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, class std::shared_ptr<const class core::io::StructFileRepOptions>, unsigned long) –> std::string

dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int) -> str
dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> str

PyRosetta-Compatible; Writes pdb data for the given residue, incrementing atom_number counter

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, unsigned long &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> std::string

dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int, out: pyrosetta.rosetta.std.ostream) -> None
dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, atom_number: int, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Writes pdb data for the given residue, incrementing atom_number counter

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, unsigned long &, std::ostream &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, out: pyrosetta.rosetta.std.ostream) -> None
dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, out: pyrosetta.rosetta.std.ostream, start_atom_number: int) -> None
dump_pdb_residue(rsd: pyrosetta.rosetta.core.conformation.Residue, out: pyrosetta.rosetta.std.ostream, start_atom_number: int, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

Writes pdb data for the given residue, beginning from the given atom number

C++: core::io::pdb::dump_pdb_residue(const class core::conformation::Residue &, std::ostream &, unsigned long, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> void

pyrosetta.rosetta.core.io.pdb.read_record_definitions_from_file(filename: str, record_type_map: pyrosetta.rosetta.std.map_std_string_core_io_pdb_RecordType) → pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t¶

Return a mapping of PDB record types to record definitions.

C++: core::io::pdb::read_record_definitions_from_file(const std::string &, const class std::map<std::string, enum core::io::pdb::RecordType, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, enum core::io::pdb::RecordType> > > &) –> class utility::vector1<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > >, class std::allocator<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > > > >

pyrosetta.rosetta.core.io.pdb.store_base_residue_type_name_in_sfr(hetID: str, text_field: str, sfr: pyrosetta.rosetta.core.io.StructFileRep) → None¶

Parse .pdb HETNAM text field to extract full resID and convert into SFR data.

C++: core::io::pdb::store_base_residue_type_name_in_sfr(const std::string &, const std::string &, class core::io::StructFileRep &) –> void

pyrosetta.rosetta.core.io.pdb.store_unknown_records_in_sfr(unknown_records: pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t, sfr: pyrosetta.rosetta.core.io.StructFileRep) → None¶

Parse and store unknown record types into SFR data.

C++: core::io::pdb::store_unknown_records_in_sfr(class utility::vector1<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > >, class std::allocator<class std::map<std::string, struct core::io::pdb::Field, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::pdb::Field> > > > >, class core::io::StructFileRep &) –> void